title: 365_364_Input

value: RPE-choroid eyecups

value: RPE Cells

value: Aldh1l1-cre/ERT2+; NuTRAP+

value: Input

value: NEBNext Ultra II Directional RNA Library Prep Kit for Illumina


title: THP1, WTvirus, undifferentiated, day8, rep1

status: Public on May 13 2024

type: SRA

city: Tucson

first: Felicia

middle: Dare

last: Goodrum

state: AZ

address: 1657 E Helen St

department: Immunobiology

country: USA

institute: University of Arizona

library_source: transcriptomic

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trimmomatic (parameters - LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36)
Trimmed sequence reads were mapped to concatenate GRCh38/CMV using STAR
Read count extraction and normalization were performed using subread
Assembly: Concatenated Homo_sapiens.GRCh38/Human herpesvirus 5 strain TB40/E clone TB40-BAC4
Supplementary files format and content: Microsoft Excel worksheet contains raw counts for each sample
Supplementary files format and content: Microsoft Excel worksheet contains RPKM values for each sample

molecule: total RNA

organism: Homo sapiens

source_name: peripheral blood

growth_protocol: THP1 monocytic cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS), βmercaptoethanol, L-glutamine and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted with the Zymo Duet Quick-DNA/RNA Miniprep kit. Manufacturer protocols were followed for column isolation of total RNA, DNAse treatment, and RNA cleaning and concentration.
cDNA libraries were prepared with an Illumina TruSeq Stranded mRNA kit and a KAPA Dual-Indexed Adaper kit. The NGS library was quantified with a qPCR-based KAPA Library Quantification kit. Manufacturer protocols were followed.

treatment_protocol: THP1 cells were cultured non-adherently for 5 days following infection (or mock infection), then treated with TPA to stimulate differentiation or with DMSO as a solvent control. Treatment was washed from cells after 24 hours.

tag: agent

tag: tissue

value: peripheral blood

tag: cell line

tag: cell type

value: monocyte

tag: genotype

tag: treatment

value: undifferentiated

tag: time


title: THP1, WTvirus, differentiated, day6, rep1

value: differentiated


title: C_4T_17

city: Orth and der Donau

first: Carolin Isabel

last: Kahlig

address: Uferstrasse 15

country: Austria

institute: Takeda

data_processing:
adapter contaminations, poly-A read-throughs and low-quanlity tails were removed using bbduk (v 38.59)
reads were mapped to GRCh38 genome using STAR aligner (v.2.7)
Count matrices were generated using HTSeq-count (v 0.12)

extract_protocol:
total RNA was harvested using Qiagen miRneasy mini plus kit
Library preparation was performed with Lexogen QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen, Austria) using 500 ng of total RNA input

value: Embryonic Kindey Cells

value: transfected


title: rTg4510+3TC [DF3]

city: Fort Collins

first: Devin

last: Wahl

state: Colorado

address: 1582 Campus Delivery, Moby Reception

institute: Colorado State University

data_processing:
Adapters trimmed & file QC by Fastp
Reads aligned with STAR and counting with LiBiNorm
Differential expression analyzed with DESeq2
Assembly: mm10

molecule: polyA RNA

organism: Mus musculus

source_name: Hippocampus

extract_protocol:
RNA for polyA RNA-seq extracted using Trizol and Zymo spin columns.
PolyA libraries were prepared according to manufacturer's instructions using the Illumina TruSeq kit

value: Hippocampus

tag: condition

tag: Sex

value: female


title: Littermate Controls [LMM2]

value: Littermate Controls

value: male


title: rTg4510+3TC [DM2]


title: C_4T_13


title: rTg4510+3TC [DF2]


title: THP1, WTvirus, undifferentiated, day6, rep1


title: VE_caMPRA_D1_rep5

city: Boston

first: Janet

last: Song

state: Massachusetts

address: 3 Blackfan St

institute: Boston Children's Hospital

data_processing:
Sequencing data from the plasmid DNA and cDNA libraries described above were processed with cutadapt to remove adapters (Martin, 2011).
Barcodes were extracted using UMI-tools (Smith et al., 2017)
Reads were mapped using bwa mem (Li and Durbin, 2009) and assigned to caMPRA probes using featureCounts (Liao et al., 2014).
The 10bp barcode were clustered to recover barcodes with small sequencing errors using the multiplexed version of the UMI-tools directional method.
Barcodes for plasmid and cDNA samples were normalized to a barcode per million format to remove bias due to sequencing coverage. Each cDNA barcode was normalized to the barcode count in the plasmid pool, and log2 transformed. Only barcodes that were found in the plasmid pool and all 5 cDNA replicate pools were used in the analysis. Enhancer activity was assessed with the XXXX test at 5% FDR.
Assembly: hg19
Supplementary files format and content: xlsx file of caMPRA results for HARs, VEs, and CNEs
Supplementary files format and content: xlsx file of random mutagenesis caMPRA results for HARs
Library strategy: MPRA

source_name: Neuro2A/N2A cells (ATCC, CCL-131)

growth_protocol: Neuro2A/N2A cells (ATCC, CCL-131) were grown in 10% fetal bovine serum, Dulbecco’s Modified Eagle Medium, and 1% Penicillin-Streptomycin in a 5% CO2 incubator at 37C.

extract_protocol:
Cell pellets were washed with 1x PBS, and mRNA was extracted using the Dynabead mRNA Direct kit (Thermo Fisher, cat #61012), according to the manufacturer’s instructions.
mRNA was reverse transcribed using Superscript VILO Master Mix with EZ DNase (Thermo Fisher, cat #11766050). caMPRA barcodes were extracted using PCR amplification with primers containing illumina adapters for both the cDNA and plasmid pools and sent out for 150bp sequencing using Hiseq instruments at Psomagen (Rockville, MD).

treatment_protocol: Molecular Inversion Probes (MIPs) targeting HARs, VEs, and CNEs were designed using the MIPgen program (Boyle et al., 2014) and manufactured as a pool by CustomArray (Bothell, WA). Target genomic sequences were captured from DNA from sample NA12878 (Coriell Institute), and the caMPRA assay then was conducted as previously described (Girskis et al., 2021). Briefly, the captures were cloned into modified pMPRA1 vector (Addgene, 49349). The only modification to the pMPRA1 vector was the addition of an AsiSI restriction site used for inserting our captured DNA fragments. The luciferase gene and minimal promoter (pMPRA_donor2, Addgene, 49353) was then cloned into the pMPRA1_Capture construct pool. For random mutagenesis, we performed error-prone PCR using the GeneMorph II Random Mutagenesis Kit (Agilent, cat #200550) on the amplified, captured sequences. N2A cells were grown as adherent cultures in 15 cm plates. Then, 15ug of MPRA constructs were transfected into cells with Lipofectamine LTX reagent (Thermo Fisher, A12621). The cells were harvested 24 or 72 hr post-transfection. Five replicates were performed per condition.

value: Neuro2A/N2A cells (ATCC, CCL-131)


title: VE_caMPRA_D1_rep4


title: C_3T_9


title: THP1, WTvirus, differentiated, day5.5, rep1


title: rTg4510  [CM1]


title: VE_caMPRA_D1_rep3


title: THP1, WTvirus, undifferentiated, day5.5, rep1


title: C_3T_5


title: VE_caMPRA_D3_rep1


title: rTg4510  [CF3]


title: VE_caMPRA_D1_rep1


title: THP1, WTvirus, undifferentiated, day5, rep1


title: rTg4510  [CF2]


title: C_3T_13


title: THP1, WTvirus, undifferentiated, day3, rep1


title: HAR_random_mutagenesis_caMPRA_rep5


title: Brain, untreated, GFP+ CD45+ CD11b+ cells

city: Stanford

first: Natalia

last: Gomez-Ospina

address: 265 Campus Drive

institute: Stanford

description:
Sample C-Naïve-MG
Cells were isolated from two mice and pooled for scRNA-seq

library_source: transcriptomic single cell

data_processing:
Raw Illumina BCL sequencing files were processed through bcl2fastq (v2.20) to generate FASTQ files   (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome)
FASTQ files were processed through Cellranger count  (v7.1.0) to obtain counts matrices
Assembly: mm10
Supplementary files format and content: Tab-separated value files and matrix files (for all samples)

source_name: Brain

extract_protocol:
The brain was minced in ice-cold HBSS 1X (Thermo Fisher Scientific 14185052), the pieces were collected by centrifugation at 400g for 5 minutes and digested using the NTDK Neural Tissue Dissociation Kit (P) (Miltenyi Biotec 130-092-628) at 37° C for 30 minutes following the manufacturer’s guidelines. Digested samples were quenched using ice-cold HBSS 1X and filtered through a 70 μm cell strainer, resuspended in 33% isotonic Percoll PLUS (GE Healthcare GE17-5445-01) and spun at 700 g for 15 minutes for myelin removal. The cell pellet was washed with FACS-BL buffer (PBS-1X supplemented with 5% Fetal Bovine Serum and 1% BSA fraction V) and kept on ice for FACS staining. Bone marrow cells (BM, from femurs and tibiae) were extracted in RPMI supplemented with 10% FBS, 4U/mL Heparin and 0.2U/mL Dnase I  and filtered using a 30 μm cell strainer and kept on ice for FACS staining. For FACS staining, cells were resuspended in 10% vol/vol Mouse BD Fc Block™ (clone 2.4G2 BD Biosciences) for 10 minutes and stained in the dark for 30 min using the following antibodies: anti-mouse CD45 PE-Cy7 (clone 104 Thermo Fisher Scientific), anti-mouse CD45 PE-Cy7 (clone 30F11 Thermo Fisher Scientific), anti-mouse/human CD11b-PE (clone M1/70 BioLegend), anti-mouse/human TER-119 PE-Cy5 (TER-119, BD Biosciences), anti-mouse Ly6C BV605 (clone AL-21 BD Biosciences), anti-mouse CD3 APC (clone 17A2 Thermo Fisher Scientific), anti-mouse CD19 PB (clone 6D3 BioLegend); eFluor™780 (Thermo Fisher Scientific 65-0865-18) was used as a viability dye. After staining, cells were washed and resuspended in FACS-BL buffer. Stained cells were sorted using a MA900 Multi-Application Cell Sorter (Sony Biotechnology) flow cytometer in cold FACS-BL buffer.
Cells were processed using the Chromium Controller and the Chromium Next GEM Single Cell 3' Reagent Kits (10x Genomics). The libraries were sequenced via Illumina Novaseq 6000 sequencer.

value: Brain

value: CD45+ CD11b+ microglia/myeloid

tag: age

value: 6 months old

tag: strain

tag: cell genotype

value: Untreated


title: C_4T_1


title: Bone marrow, conditioned and transplanted, GFP+ CD45+ CD11b+ cells

description:
Sample D-BM-CD11b+
Cells were isolated from two mice and pooled for scRNA-seq

source_name: Bone  marrow

value: Bone  marrow

value: CD45+ CD11b+ myeloid

value: Busulfan + PLX3397 + Bone Marrow Transplant


title: HAR_random_mutagenesis_caMPRA_rep3


title: THP1, uninfected, differentiated, day8, rep1

value: peripheral blood

value: monocyte

value: mock


title: C_3T_1

value: Embryonic Kindey Cells


title: HAR_random_mutagenesis_caMPRA_rep4


title: C_2T_5

value: transfected


title: THP1, WTvirus, undifferentiated, day1, rep1

value: undifferentiated


title: HAR_random_mutagenesis_caMPRA_rep2


title: rTg4510  [CM3]

value: Hippocampus


title: Brain, conditioned and transplanted, GFP- CD45+ CD11b+ cells

description:
Sample B-Host-MG
Cells were isolated from two mice and pooled for scRNA-seq

value: female

value: C57BL/6J (WT)


title: THP1, uninfected, differentiated, day6, rep1

value: differentiated


title: VE_caMPRA_D1_rep2

value: Neuro2A/N2A cells (ATCC, CCL-131)


title: C_2T_17


title: Tumor, Prot_8.1

city: Bethesda

first: Anish

last: Thomas

state: MARYLAND

address: Center for Cancer Research, National Cancer Institute, Building 10 Room 4-5330

department: National Cancer Institute

institute: National Institutes of Health

data_processing:
STAR
Trimmomatic, aligned and count matrix generated using Rsubread
Assembly: hg38
Supplementary files format and content: count matrix

source_name: Liver

extract_protocol: RNA was extracted from FFPE tumor cores (n= 12 samples) using RNeasy FFPE kits according to the manufacturer’s protocol (QIAGEN, Germantown, MD). RNA-seq libraries were generated using Truseq RNA Access Library Prep Kits (TruSeq RNA Exome kits; Illumina) and sequenced on Highseq3000 sequencers using 75 bp paired-end sequencing method (Illumina, San Diego, CA). For transcriptomic analyses, raw RNA-Seq count data were normalized for inter-gene/sample comparison using FPKM, followed by log2(x + 1) transformation, as implemented in the edgeR R/Bioconductor package

value: Liver

value: Male


title: Brain, conditioned and transplanted, GFP+ CD45+ CD11b+ cells

description:
Sample A-MGLCs
Cells were isolated from two mice and pooled for scRNA-seq

value: Brain

value: CD45+ CD11b+ microglia/myeloid

value: 6 months old


title: THP1, uninfected, undifferentiated, day6, rep1


title: HAR_random_mutagenesis_caMPRA_plasmid_DNA


title: HAR_random_mutagenesis_caMPRA_rep1


title: C_2T_9


title: C_3T_17


title: Tumor, Prot_6.1


title: C_2T_13


title: THP1, uninfected, differentiated, day5.5, rep1


title: C_2T_1


title: HAR_caMPRA_plasmid_DNA


title: THP1, uninfected, undifferentiated, day8, rep1


title: Tumor, Prot_5.2


title: C_1T_9


title: HAR_caMPRA_D3_rep5


title: THP1, uninfected, undifferentiated, day5.5, rep1


title: Tumor, Prot_5.1

source_name: Lung

value: Lung


title: HAR_caMPRA_D3_rep4


title: THP1, uninfected, undifferentiated, day5, rep1

value: peripheral blood


title: HAR_caMPRA_D3_rep3


title: Tumor, Prot_3.2

value: Female


title: Tumor, Prot_4.1


title: C_1T_17


title: C_1T_5


title: THP1, uninfected, undifferentiated, day3, rep1

value: monocyte

value: mock


title: C_1T_13

value: Embryonic Kindey Cells

value: transfected


title: THP1, uninfected, undifferentiated, day1, rep1

value: undifferentiated


title: HAR_caMPRA_D3_rep2


title: Tumor, Prot_2.1


title: C_1T_1


title: HAR_caMPRA_D3_rep1


title: Tumor, Prot_2.2


title: Tumor, Prot_2.3


title: SSCS7

city: Charleston

first: Carol

last: Feghali-Bostwick

state: SC

address: 96 Jonathan Lucas St room 822

department: Medicine

institute: Medical University of South Carolina

data_processing:
Novogene: Original image data file from HTS platforms is transformed to sequenced reads ( Raw Data or Raw Reads) by CASAVA base recognition (Base Calling).
Raw data are stored in FASTQ(fq) format files, which contain sequences of reads and corresponding base quality.
STAR software is used to accomplish the mapping. The alignment by STAR precisely and effectively performs positioning junction reads for RNA sequencing data analysis.
Gene expression level is calculated by the number of mapped reads with FeatureCounts. Read counts is proportional to gene expression level, gene length and sequencing depth, and is used for DE analysis.
Gene-level count data were generated by HTSeq and FeatureCounts. DE analysis of two conditions/groups was performed using the DESeq2 R package (Anders et al., 2010). Significance criteria q-value<0.05, log2FC>0.6 upregulation, log2FC<-0.6 downregulation
Assembly: Homo Sapiens(GRCh38/hg38)
Supplementary files format and content: tab-delimited .txt files generated by DESEQ2

source_name: pericytes SSc lung (SSCL)

growth_protocol: Tissue was processed for cell culture and selection of PDGFRβ+ cells as described previously. Briefly, minced and enzymatically digested lung tissue was plated on 0.2% gelatin-coated dishes in a specialized, low-serum (2% FBS) medium conducive for pericyte growth (Pericyte Medium; ScienCell, Carlsbad, CA, catalog #1201).

extract_protocol:
Aurum™ Total RNA Mini kit (Bio-Rad, Hercules, CA) in conjunction with DNase treatment as per the manufacturers' specifications.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA library prep kit for Illumina (NEB, USA).

value: lung

value: pericytes

tag: disease state

value: SSCL


title: HAR_caMPRA_D1_rep4

value: Neuro2A/N2A cells (ATCC, CCL-131)


title: HAR_caMPRA_D1_rep5


title: SSCS9


title: Tumor, Prot_11.1

value: Liver


title: Tumor, Prot_10.1


title: 30_100_2

city: Wuhan

first: Zhen-Xia

last: Chen

state: Hubei

address: No.1 Shizishan Street

department: College of Life Science and Technology

country: China

institute: Huazhong Agricultural University

description: mixed species RNA preparation prepared with zebrafish RNA

data_processing:
RNA-Seq: High-throughput sequencing raw image data files were converted to reads using fqtools_plus analysis.
RNA-Seq: We used FastqC (0.11.8) to evaluate the raw reads quality. Sequencing report tool was MultiQC (0.9).
RNA-Seq: Reads were mapped to the corresponding reference genomes (flybase dm6) by Hisat2 (2.0.5) with parameters “-x --rna-strandness RF” and “--known-splicesite-infile” followed by gene annotation in GTF format
RNA-Seq: The output of Hisat2 were converted to BAM format, sorted and reads with MAPQ <30 were discarded by Samtools (1.7)
RNAseq: HTSeq (0.9.1) was used for counting reads with parameters “-t exon -i gene_id -r name -s reverse”.
Genome_build: Dm6
Supplementary_files_format_and_content: Tab-delimited text files include raw or normalized read counts of all the genes for each RNAseq sample.

organism: Drosophila melanogaster

source_name: TMPyP4 100umol replicates2

growth_protocol: Drosophila line 2 cells (S2) were maintained at 28°C in Hyclone TNM-FH insect medium containing 10% Gibico serum and antibiotics (0.5 U/ml penicillin and 0.5 μg/ml streptomycin).

extract_protocol:
We extracted the total RNA using the Trizol method. We added 1 ml of Trizol (invitrogen) to the sample (4-7 million cells) stored at -80 ° C, and carefully piped the sample with a pipette, which was the homogenate of the tissue cells. Then, 200 μl of chloroform was added to the homogenate, and the sample was shaken for 15 seconds using a vortex shaker until the phase separation disappeared. After standing at room temperature for 2-3 minutes, the sample was centrifuged at 12,000 g for 15 minutes at 4 °C. The colorless supernatant was transferred to another new centrifuge tube, mixed well with an equal volume of isopropanol, held at -20 ° C for 10 minutes, and then centrifuged at 12,000 g for 10 minutes at 4 ° C to precipitate RNA. The supernatant was carefully removed, the precipitate was gently washed 2-3 times with 1 ml of fresh 75% ethanol, dried at room temperature for 2 to 3 minutes and dissolved in 50 μl of RNase-free water.
Stranded PolyA+ RNA libraries were prepared at Majorbio (Shanghai, China) with in-house kits. A total of 12 qualified cDNA libraries were constructed and were sequenced on the Illumina HiSeq XTen System (Illumina Inc., San Diego, CA).

treatment_protocol: S2 cells were treated with different concentration of TMPyP4 (25μmol/L, 50μmol/L, 100μmol/L, respecticely), and DMSO was severed as control. After 48 hours, the S2 cells were sampled for sequencing.

tag: drug concentration

value: 100 micromol/L

tag: library type

value: fr-firststrand (dUTP)


title: 6_50_1

source_name: TMPyP4 50umol replicates1

value: 50 micromol/L


title: 66_25_2

source_name: TMPyP4 25umol replicates2

value: 25 micromol/L


title: NORMS15

source_name: pericytes normal lung (NORML)

value: NORML


title: 54_C3

source_name: DMSO 100μg/L replicates3

value: 100 microgram/L

value: DMSO


title: HAR_caMPRA_D1_rep3


title: SSCS2


title: NORMS8


title: Tumor, Prot_1.1

value: Male


title: HAR_caMPRA_D1_rep2


title: HAR_caMPRA_D1_rep1


title: 78_25_1

source_name: TMPyP4 25umol replicates1


title: NORMS10


title: 18_C2

source_name: DMSO 100μg/L replicates2


title: PEA1 rAREG 3

type: RNA

city: Providence

first: Nicole

middle: Elizabeth

last: James

state: Rhode Island

address: 200 Chestnut Street

department: OB/GYN

institute: Women and Infants Hospital

description: low count genes were filtered out for a total of 750 genes detected on the panel

hyb_protocol: The reporter code set and capture probe set tubes were removed from -80C and thawed on ice, prior to mixing by tapping and pulse centrifugation. 70 µl hybridization buffer was added to the tube containing the reporter probe set and mixed by tapping, followed by pulse centrifugation. 8 µl of the diluted reporter probe was added to a PCR tube. Each RNA sample was diluted in water to 25 ng/µl and 2 µl final volume for 50 ng total input per sample. 5 µl RNA sample was added to each tube containing the reporter probe set and mixed by tapping, followed by pulse centrifugation. 2 µl Capture Probe Set was added to each tube, mixed by tapping, and the sample was collected by pulse centrifugation and then immediately placed in a pre-heated PCR machine, with the lid set to 70 °C and the block set to 65 °C. The hybridization was performed for 18 h at 65 °C. Samples were cooled to 4 °C and any condensation was collected by pulse centrifugation. Each sample was diluted with 18 µl hybridization buffer.

scan_protocol: An nCounter Sprint cartridge was calibrated to room temperature for 15 min prior to injection of 33 µl of each sample into one of the 12 injection ports of the cartridge, followed by the introduction of an air seal. The sample injection cartridge was sealed with provided tape and the reagent supply ports were unsealed prior to loading on the nCounter Sprint profiler. The analysis run was started immediately after loading.

data_processing: The resulting data fole in RCC format was used for data analysis in the ROSALIND analysis platform. Raw data in RCC format was uploaded in ROSALIND for automated normalization, background subtraction, and quality control (QC) check.

label: fluorescent barcode

source_name: PEA1 cell line

growth_protocol: OVCR8WT cells were cultured in Dulbecco Modified Eagle Medium supplemented with 10% Fetal Bovine Serum (FBS) and 1% penicillin/streptomycin. PEA1 cells were grown in RPMI 1640 supplemented with 2mM of glutamine, 2mM of sodium pyruvate, 10% FBS, and 1% penicillin/streptomycin. Cells were maintained in a 37°C/5% CO2 humidified chamber.

extract_protocol: RNA was isolated using Trizol / LiCL extraction/precipitation protocol.

treatment_protocol: OVCAR8WT and PEA1 cells were treated with either BSA control (samples 1-3 and samples 7-9) or 200ng/ml of rAREG (samples 4-6 and samples 10-12) for 2 hours .


title: 162_50_2

source_name: TMPyP4 50umol replicates2


title: NORM2


title: 174_100_3

source_name: TMPyP4 100umol replicates3


title: CNE_caMPRA_plasmid_DNA


title: CNE_caMPRA_D3_rep5


title: CNE_caMPRA_D3_rep4


title: CLU_2

city: Guangzhou

first: by

last: h

address: Guangzhou, Guangdong Province

institute: Jinan University

data_processing:
The Cell Ranger takes FASTQ files and performs alignment, filtering, barcode counting, and UMI counting
The Seurat analyses data
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: IOMM-LEE cells

extract_protocol:
The isolation of single cells was conducted in a sterile environment with the instruments pre-autoclaved and the solutions filtered through a 0.22μm filter. The fresh human meningioma tissues were put in cold L-isolation buffer (DPBS, 0.9mm CaCl2, 0.49mm MgCl2, 25mm D-glucose, then 1mm Sodium pyruvate), cut into small blocks of 3–5mm3 with a surgical blade, and placed after upside-down using pre-cooled PBS in a 50ml centrifuge tube. After most of the lumps sank, the supernatant containing a large number of cells related to the hematological system was discarded and repeated three to five times to obtain a relatively pure meningioma tissue mass. The tissue masses were placed in Petri dishes, minced as much as possible with a surgical blade, and transferred to a pre-cooled L-isolation buffer, where Dounce Tissue Grinder (Wheaton) was used to further mill the tissue masses into tissue suspension. The suspension was centrifuged at 2000g for 10 minutes and resuspended in a WASH buffer (L-isolation buffer containing 10% BSA). A 100μm cell screen was used for filtration to remove the uncrushed lumpy tissue and the filtrate was further filtered through a 40μm cell screen (Falcon) to obtain a crude cell suspension. After the crude suspension was washed twice with pre-cooled HBSS containing calcium and magnesium, the precipitate was resuspended in Digesting Buffer I (HBSS, 4%Dispase, 1mg/mL Collagen ASE I, 1mg/mL Collagen ASE II, 1mg/mL Collagen ASE IV, 5μg/mL DNA ASE I) and digested slowly in a rotating oven at 37°C for 1h. After digestion, the samples were centrifuged at 500g for 5 minutes at low temperature, and the cell pellets were washed twice with HBSS and re-suspended in Digest Buffer II (HBSS, Neurological Isolation Enzyme, 5μg/mL DNA ASE I) for digestion by slow rotation in an incubator at 37°C for 1h. Once the digestion was complete, the filtrate was filtered through a 15μm cell screen (Pluriselect) and the filtrate became the single-cell suspension. After low-temperature centrifugation, the single-cell suspension was re-suspended in L-isolation buffer, and then every 700g/μl of suspension was slowly added to 1.6ml of L-isolation buffer containing 20%percoll, and the suspension was centrifuged at 0, 700g for 10 min to remove tissue debris and dead cells. The cell precipitate was directly resuspended in erythrocyte lysis buffer, treated at normal temperature for 10 minutes, washed with PBS twice, and then re-suspended in pre-cooled PBS. The obtained meningioma single cells were used for single-cell sequencing. For the primary culture of meningioma cells, the tissues were directly cut into pieces, added to a DMEM medium containing 10mg/ml Collagenase I and 5%FBS, and placed in an incubator at 37°C for digestion for 1h, during which the tissues were gently blown several times every 10 minutes using a Pap pipette. The digested cells were stripped of red blood cells with red blood cell lysates, washed twice with PBS, and resuspended in DMEM/F12 (3: 1) medium containing 10%FBS(Gbico), 10% HS (Horse serum) and 1% p/s. Cells were incubated at 37°C with 5% CO2 and the medium was changed every three days.
According to the manufacturer’s instructions, single-cell libraries were generated via the Chromium Controller and the Single Cell Reagent Kit 3’ v3 (10x Genomics, Pleasanton, CA),RNA libraries were prepared for sequencing using standard Illumina protocols

value: IOMM-LEE cells

value: overexpression


title: 150_100_1

source_name: TMPyP4 100umol replicates1


title: 126_C1

source_name: DMSO 100μg/L replicates1


title: PEA1 rAREG 2


title: CNE_caMPRA_D3_rep3

source_name: Neuro2A/N2A cells (ATCC, CCL-131)


title: PEA1 rAREG 1


title: CNE_caMPRA_D3_rep2


title: sgC_3

value: knock-out


title: CLU_1


title: CNE_caMPRA_D3_rep1


title: 102_50_3

source_name: TMPyP4 50umol replicates3


title: PEA1 control 3


title: PEA1 control 2


title: sgC_2


title: sgC_1


title: CNE_caMPRA_D1_rep4


title: CLU_3


title: WT_3

value: Wide Type


title: CNE_caMPRA_D1_rep5


title: PEA1 control 1


title: OVCAR8 rAREG 3

source_name: OVCAR8WT cell line


title: OVCAR8 rAREG 2


title: 114_25_3

source_name: TMPyP4 25umol replicates3


title: OVCAR8 rAREG 1


title: WT_2


title: CNE_caMPRA_D1_rep2


title: WT_1


title: 489180-T

city: Beijing

first: Zhidong

last: Wang

address: Yard 27, Taiping Road, Haidian district

institute: Graduate Collaborative Training Base of Academy of Military Sciences, Hengyang Medical School, University of South China

description: Test

data_processing:
The matrix non-normalized data was the Ct value of  snoRNA in each group performed with qPCR. The matrix normalized data was calculated for each gene in each group according to the ΔCt method. ΔCt = Ct – HK genes’ Ct  The fold change was calculated for each gene from group test to group control as 2^-ΔCt(test)/2^-ΔCt(control).
sample data table reports normalized signal (against housekeeping genes). Fold Change worksheet reports test/control (i.e., tumor tissues/normal tissues) ratios.

label: SYBR Green

source_name: Tumor tissues

label_protocol: Reverse transcription was performed using rtStar™ First-Strand Synthesis Kit (Cat# AS-FS-001, Arraystar) following the Manufacturer’s instructions. Quantitative real-time PCR were performed  with 45 cycles at 95 ℃ for 15 seconds and 60 ℃ for 60 seconds using Arraystar SYBR® Green qPCR Master Mix(ROX+) (AS-MR-006-5, Arraystar).

extract_protocol: Total RNA was extracted with TRIZOL followed by DNase I treatment.

tag: cancer type

value: colorectal cancer

value: Tumor tissue


title: 487416-T

description: Test


title: 489005-T

description: Test


title: 487416-C

description: Control

source_name: Compared normal tissues

value: normal tissue


title: CNE_caMPRA_D1_rep1

value: Neuro2A/N2A cells (ATCC, CCL-131)


title: 489180-C

description: Control


title: OVCAR8 control 2


title: OVCAR8 control 1


title: ATAC-seq: H1-ESC, rep1

status: Public on May 12 2024

first: William

middle: James

last: Greenleaf

state: CA

address: Beckman Center B-279, Campus Drive West

department: Genetics

institute: Stanford University

description:
H1.Tn5shift.insertion.coverage.bigwig
overlap.optimal_peak.narrowPeak.gz
overlap.optimal_peak.narrowPeak.bb

library_source: genomic

data_processing:
To get all processed files we input the fastqs to ENCODE ATAC-seq piepline caper (V2.1.2).
Assembly: GRCh38 (https://www.encodeproject.org/references/ENCSR938RZZ/)
Supplementary files format and content: Output of ENCODE ATAC-seq pipeline (https://github.com/ENCODE-DCC/atac-seq-pipeline) - peak calls in narrowpeak format, fold-enrichment bigiwg and p-value bigiwig

molecule: genomic DNA

extract_protocol:
Cryopreserved cells were thawed using standard procedures and treated with DNase I for 30 minutes to remove extracellular DNA from dead cells, then Ficoll purified. ATAC-seq experiments was performed following the omniATAC protocol. Briefly, ~70,000 cells were centrifuged at 500 g, then resuspended in 1 mL 1x PBS and centrifuged again. Cells were then resuspended in 50 uL ATAC-RSB-Lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630, 0.1% Tween-20) and incubated on ice for 3 minutes. Subsequently 1 mL ATAC-RSB-Wash buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20) was added, the tubes were inverted several times, and nuclei were centrifuged at 500 g for 5 min at 4C. Transposition was carried out by resuspending nuclei in a mix of 25 uL 2x TD buffer (20 mM Tris-HCl pH 7.6, 10 mM MgCl2, 20% Dimethyl Formamide), 2.5 uL transposase (Illumina) and 22.5 uL nuclease-free H2O, and incubating at 37C for 30 min in a Thermomixer at 300 rpm.
Transposed DNA was isolated using the MinElute PCR Purification Kit (Qiagen Cat# 28004/28006), and PCR amplified for a custom number of cycles for each library that yields ~1/4 of plateau SYBR green fluorescene in a pilot 5 µL qPCR reaction (~10 cycles) using the usual ATAC-seq settings.

value: Human Embryonic Stem cells (hESC)


title: ATAC-seq: H1-ESC, rep2


title: 489005-C

description: Control


title: Control

city: New York

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

data_processing:
Data were processed using CellRanger count Version 7, with the hybrid (Human+Mouse) reference
Assembly: refdata-gex-GRCh38-and-mm10-2020-A
Supplementary files format and content: tar file containing all tab-separated values files and matrix files

source_name: Cell line xenograft

growth_protocol: 4-10 male 6-week-old NOD.Cg-Prkdc<scid> Il2rg<tm1Wjl>/SzJ (NSG) mice were subcutaneously engrafted per treatment arm and until tumors reached 100-150 mm3.

extract_protocol:
Upon delivery to the lab, samples were mechanically/enzymatically dissociated using the tumor dissociation kit (#130-095-929, Miltenyi) and the GentleMACS Octo Dissociator with Heaters (Miltenyi, # 130-096-427). Resection samples were chopped and added to 7.5 mL of enzyme mix in the GentleMACS tube, while core needle biopsies/fine needle aspiration samples were added to 2.5 mL of enzyme mix in the GentleMACS tube. After 15-30 minutes dissociation, depending on sample size and consistency, bigger size samples were filtered with MACS SmartStrainers (70 μm) (Miltenyi, #130-098-462) into 50 mL tubes, and smaller samples were filtered with 35 uM stainer cap FACS tube (Corning # 352235). Then, samples were centrifuged (800g, 1 minute) and supernatant was discarded. Pelleted cells were then stained as indicated below. Cell pellet was resuspended in 200-3000 uL of Red Blood Cell Lysis Solution (ACK lysis buffer), depending on the pellet size. After incubation for 2 minutes at room temperature the ACK buffer was diluted 10-times with 1X PBS containing 2.5% FBS and pelleted again. Cell pellet was resuspended in 100 uL of 1X PBS + 2.5% FBS, mixed with 5 uL of Human TruStain FcX (Biolegend #422302), 3 uL of PE H2KD antibody 0.1 uL of calcein (1μg/μL, Calcein (Biolegend #425201)), and left for 15 minutes on ice. Stained samples were washed twice with 2 ml of 1X PBS + 2.5% FBS, and finally resuspended in the same buffer supplemented with DAPI dye. Using BD FACSAria (BD Biosciences) or Sony MA900 (Sony) flow cytometers, cells were sorted on DAPI-, Calcein+ (FITC+) to select for live cells. In addition, we sorted only H2KD- (human cells).
FACS-sorted cells were subjected to scRNA-seq protocol using Chromium (10X genomics) instrument and Single Cell 3’ Reagent Kit (v3). Each sample, containing approximately 3000-8000 cells was encapsulated and barcoded following the manual (CG000183 Rev B). The viability of samples varied between 58-98% (median 80%), as confirmed with 0.2% (w/v) Trypan Blue staining. The final sequencing libraries were double-size purified (0.6–0.8X) with SPRI beads and sequenced on Illumina Nova-Seq platform (R1 – 26 cycles, i7 – 8 cycles, R2 – 70 cycles or higher). On average, 3,330 cells per clinical sample (N = 62) were sequenced at a depth of ∼42.000 reads per cell (195 million reads per sample). The unique mapping was high, between 79-88%, and a median number of unique transcripts per cell was 4.393.

treatment_protocol: mice were randomized into groups and treated with either vehicle, simurosertib (40 mg/kg p.o. QDx3), enzalutamide (10 mg/kg p.o. QDx5), osimertinib (25 mg/kg p.o. QDx5) or their combination.

value: Cell line xenograft

value: LnCap/AR DKO

value: Prostate adenocarcinoma


title: Enzalutamide

value: Enzalutamide


title: Simurosertib

value: Simurosertib


title: P5C

city: Madison

first: Bridget

middle: E.

last: Shields

state: Wisconsin

address: 1 S Park Street

department: Department of Dermatology

institute: University of Wisconsin School of Medicine and Public Health

description: fresh frozen spatial transcriptome sequencing

data_processing:
Raw FASTQ files were processed using Space Ranger (v 1.2.2) count command with default parameters, against Grch38-2020-A, a reference genome which can be downloaded from 10x Genomics website.
Assembly: Grch38-2020-A, a reference genome which can be downloaded from 10x Genomics website.
Supplementary files format and content: barcode.tsv.gz list of spatial barcodes
Supplementary files format and content: features.tsv.gz list of gene Ids
Supplementary files format and content: matrix.mtx.gz gene expression count data in Matrix Market Exchange format
Supplementary files format and content: detected_tissue_image.jpg Image of tissue and spots
Supplementary files format and content: scalefactors_json.json scale factos in json format
Supplementary files format and content: tissue_hires_image.png high resolution tissue image
Supplementary files format and content: tissue_lowres_image.png low resolution tissue image
Supplementary files format and content: tissue_positions_list.csv spot position coordinates in csv format

source_name: Skin

growth_protocol: No growth protocol as this was fresh skin tissue

extract_protocol:
Fresh frozen tissues were OCT embedded, and 10 μm frozen sections were cut with cryostat
Spatial transcriptome sequencing libraries were prepared with 10x Genomics Visum Spatial Gene Expression Slides and Reagent kit according to manufacturer's construction
Spatial transcriptomics

treatment_protocol: No treatment protocol

value: Skin

value: Control


title: CNE_caMPRA_D1_rep3


title: P6C


title: K562 Hi-C rep2

city: St. Louis

first: SIQI

last: ZHAO

state: MO

address: Campus Box 8232 4515 McKinley Ave.

institute: Washington University in St. Louis

data_processing:
The reads were then processed with the Juicer pipeline56 to generate HiC contact files for each replicate. We then used the peakHiC tool57 to call loops from each IR with the following parameters: window size = 80, alphaFDR = 0.5, minimum distance = 10kb, qWr = 1. Using these parameters each IR was looped to a median of 3 regions (range 0-7).
Assembly: hg38
Supplementary files format and content: Hi-C data is stored as contact map .hic format.

growth_protocol: K562 cells were cultured using a medium consisting of Iscove’s Modified Dulbecco’s Medium (IMDM) + 10% Fetal Bovine Serum (FBS) + 1% non-essential amino acids + 1% pen/strep at 37 C with 5% of CO2. HEK293 cells were cultured using a medium consisting of Eagle’s Minimum Essential Medium (EMEM) + 10% Fetal Bovine Serum (FBS) + 1% pen/strep at 37 C with 5% of CO2.

extract_protocol: We performed Hi-C on wild-type K562 cells with the Arima Hi-C kit (A510008) according to the manufacturer's protocols (3 replicates, 870 million reads total).


title: K562 Hi-C rep3


title: P4C


title: K562 Hi-C rep1


title: OVCAR8 control 3


title: P5A

value: Affected


title: P3C


title: P4A


title: P3A


title: Library_6A_7659

city: Chicago

first: Alexander

middle: V.

last: Misharin

state: IL

address: 303 E Superior

institute: Northwestern University

data_processing:
Reads were aligned to a custom built genome (human GRCh38.93 and SARS-CoV-2 NC_045512.2) and counted by gene by cell with cellranger count command (v7.0.0 exon-only mode), producing raw and filtered gene expression matrices.
Assembly: custom (human GRCh38.98 and SARS-CoV-2 NC_045512.2)
Supplementary files format and content: gene expression count matrices

source_name: Sorted macrophages and T cells

extract_protocol: Libraries were prepared with 10x Genomics 5' V2 gene expression (GEX) reagents according to the manufacturer protocol (CG000331_RevA).

tag: sample

value: Positive


title: P1C


title: P1A


title: Library_5E_4601


title: Combo

value: Combo


title: P2A


title: Library_4A_5368


title: Library_0K_8030


title: Library_3G_4001


title: P6A


title: Library_2D_2348


title: Library_2N_7756


title: Library_1B_3418


title: Library_8V_4438


title: Library_9V_1779


title: Library_2K_0330


title: Library_4T_2687


title: Library_4S_4889


title: Library_0C_0494


title: Library_3Z_9302


title: P2C


title: Library_3K_1499


title: Library_5D_3628


title: Library_8H_5846


title: Library_6A_3748

source_name: Nasal epithelium


title: Library_7N_2251


title: Library_4V_0698


title: Library_6H_5843


title: Library_5D_4720


title: Library_2I_1950


title: Library_7Z_5659


title: Library_8D_7722


title: Library_2V_9976


title: Library_1C_7685

value: Negative


title: Library_4G_4392


title: Library_6Y_4795


title: Library_1Y_7124


title: Library_0Y_1813


title: Library_6G_9945


title: Library_5J_0421


title: Library_1X_2236


title: Library_4R_4787


title: Library_3Y_4791


title: Library_1O_1165


title: Library_3Q_0337


title: Library_5O_4978


title: Library_4R_2600


title: Library_0X_7593


title: dosR mutant Rep 2, Artemisinin treated

city: East Lansing

first: Robert

middle: B.

last: Abramovitch

state: MI

address: 567 Wilson Road

department: Microbiology and Molecular Genetics

institute: Michigan State University

data_processing:
Illumina bcl2fastq (v1.8.4) was used to de-multiplex and convert reads to FASTQ format
Reads from each lane were combined into individual files using standard UNIX commands
Paired-end reads were trimmed to remove low quality bases (Phred score < 20) and Illumina adapters using TrimGalore!  (v0.6.4) and cutadapt  (v2.6).
Next, trimmed reads were pseudoaligned to the M. abscessus ATCC 19977 ASM6918v1 cDNA reference from Ensembl using Kallisto  (v0.46.0). The index was prepared using a k-mer size of 31. Pseudoalignment and transcript abundance quantification was performed using the Kallisto quant subcommand with default parameters and the following modifications: 1) -b 500, 2) --rf-stranded, 3) --genomebam, and 4) --gtf Mycobacterium_abscessus_atcc_19977.ASM6918v1.45.gtf. The aforementioned modifications are to accommodate 1) 500 bootstraps for transcript abundance estimation, 2) reverse-stranded libraries, and 3-4) for generation of a genome BAM.
Transcript abundance counts were imported and summarized to the gene level using the R (v3.6.1) package tximport  (v1.14.0).
Libraries were normalized for effective library size and effective gene length output from Kallisto using edgeR  (v3.28.0) and csaw  (v1.20.0).
Samples were filtered on a genewise basis requiring at minimum 1 count per million (CPM) in at least 2 samples. Differential gene expression was performed using edgeR’s quasi-likelihood framework, estimating dispersions and negative binomial generalized linear model fits with the robust flag set to TRUE.
Statistical significance was determined using quasi-likelihood F-tests and a Storey’s q-value  less than 0.05.
Genome_build: M. abscessus ATCC 19977 ASM6918v1
Supplementary_files_format_and_content: Processed files are presented as .xlsx spreadsheets and represents the average of 2 biological replicates

organism: Mycobacteroides abscessus ATCC 19977

source_name: Bacterial Cell

growth_protocol: WT or DosR deletion mutant were cultured in 16 mL of Dubos browth +10% ADS and 0.05% Tween 80 starting at an OD of 0.05  in a T-25 flask (in horizontal position). The cultures were treated with 20 uM artemisinin or a DMSO control for 24 hours, RNA was extracted, llibraries generated, sequenced and differential gene expression analyzed.

extract_protocol:
The cultures were treated with 2 volumes of GTC buffer and collected by centrifugation . Cells were lysed using a bead beater. Total RNA was prepared from the pellets using the Direct-zol™ RNA Miniprep kit.
cDNA libraries were constructed using the Illumina TruSeq RNA library preparation kit (v2), omitting the polyA selection step. Multiplexing sequences are included in the title of the associated fastq.gz files.
After library quality control, sample libraries were pooled and sequenced in two lanes of an Illumina HiSeq 2500 Rapid Run flow cell (v1) in 50bp, paired-end read format (SE50). After the sequencing run, reads were de-multiplexed and converted to FASTQ format using the Illumina bcl2fastq (v1.8.4) script.

treatment_protocol: The cultures were treated with 20 uM artemisinin or a DMSO control for 24 hours.

tag: genotype/variation

value: espM deletion mutant

tag: agent

value: Artemisinin


title: Library_2J_4670


title: dosR mutant Rep 1, Artemisinin treated


title: Library_8F_2235


title: dosR mutant Rep 1, DMSO

value: dosR deletion mutant

value: DMSO


title: HSC3 cells, suspended, 7th days, rep3

city: Hangzhou

first: Jiong

last: Lyu

state: Zhejiang

address: Rd.Yuhangtang  866

institute: Zhejiang University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Supplementary files format and content: txt (fpkm for all gene in 12 samples)

source_name: Tongue cancer

growth_protocol: CAL27 and HSC3 were maintain in DMEM/F12 with 10% FBS in humidified atmosphere with 5% CO2 at 37C;

extract_protocol:
RNA was harvested using trizol（Ambion/Invitrogen，USA）. 2 ug of total RNA was used for the construction of sequencing libraries.
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR  primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: For adherent culture, the culture condtion is like above, for suspension culture, CAL27 and HSC3 were seeded in DMEM/F12 with 2% B27, 10ng/ml EGF and 10ng/ml bFGF in low adhesion culture plate at density of 100000 cells/ml, the culture medium is refresh every three days

tag: tissue

value: Tongue cancer

tag: cell line

value: squamous cell carcinoma

tag: culture

value: Suspension


title: dosR mutant Rep 2, DMSO


title: HSC3 cells, suspended, 7th days, rep1

tag: cell type


title: WT Rep 1, Artemisinin treated

value: Wild Type


title: HSC3 cells, adherent, at logarithmic period, rep1

value: Adherent


title: HSC3 cells, adherent, at logarithmic period, rep2


title: HSC3 cells, adherent, at logarithmic period, rep3


title: CAL27 cells, suspended, 7th days, rep3


title: WT Rep 1, DMSO


title: Library_0K_9516


title: Library_2Q_8010


title: WT Rep 2, DMSO


title: CAL27 cells, adherent, at logarithmic period, rep3


title: CAL27 cells, suspended, 7th days, rep2


title: Blank control replicate3

first: Boan

last: Li

address: Baili Street and Qingfeng West Road in Tiangongyuan Street

institute: the Fifth medical center of Chinese PLA General Hospital

data_processing:
Sequence reads were trimmed adaptor/low-quality sequences using cutadapt v3.4
Trimmed sequence reads were mapped to Grch38/hg38 using HISAT2 v2.2.1 (parameters-mismath cost:1)
Read count extraction were performed using featureCounts v2.0.1
Assembly: Grch38
Supplementary files format and content: Comma separator csv file includes raw counts for all samples

growth_protocol: HCT-116 cells were maintained in DMEM supplemented with 10% exosome-depleted serum and 1% antibiotics in humidified atmosphere with 5% CO2 at 37 ℃.

extract_protocol:
RNA was extracted using RNeasy Mini Kit (Qiagen).
RNA libraries for RNA-seq were prepared using NEBNext Ultra II RNA Library reagent kit following manufacturer's protocols.

treatment_protocol: HCT-116 cells were treated with different concerntrations of EVs from HCC patients serum or healthy peopele serum.

value: epithelial-like cell

tag: treatment

value: 0 mg/mL


title: Blank control replicate1


title: Blank control replicate2


title: CAL27 cells, suspended, 7th days, rep1


title: ecopic endometrium, patient 12

city: xiamen

first: Mengjie

last: Yang

state: Fujian

address: 66 Zhenhai Road, Siming District, Xiamen City, Fujian Province, China

department: National Institute for Data Science in Health and Medicine

institute: School of Medicine, Xiamen University

data_processing:
Raw data of FASTQ format were then processed.
In this step, remove the adapter sequence and filter out low quality (low quality, the number of lines with a string quality value less than or equal to 25 accounts for more than 60% of the entire reading) and N (N means that the base information cannot be determined) ratio is greater than 5% reads to obtain clean reads that can be used for subsequent analysis.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software (http://daehwankimlab.github.io/hisat2/) to obtain mapped reads. FeatureCounts (http://subread.sourceforge.net/) was used to count the reads numbers mapped to each gene.
And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: Homo_sapiens.GRCh38.p13
Supplementary files format and content: tab-delimited text files include count and FPKM values for each Sample

source_name: endometrium

extract_protocol:
Total RNA was extracted from the endometrial tissues using TRIzol® Reagent according the manufacturer’s instructions (Magen). RNA samples were detected based on the A260/A280 absorbance ratio with a Nanodrop ND-2000 system (ThermoFisher Scientific, USA), and the RIN of RNA was determined by an Agilent Bioanalyzer 4150 system (Agilent Technologies, CA, USA). Only qualified samples will be used for library construction.
Paired-end libraries were prepared using an ABclonal mRNA-seq Lib Prep Kit (ABclonal, China). The mRNA was purified from 1 μg total RNA using oligo (dT) magnetic beads followed by fragmentation carried out using divalent cations at elevated temperatures in ABclonal First Strand Synthesis Reaction Buffer. Subsequently, first-strand cDNAs were synthesized with random hexamer primers and Reverse Transcriptase (RNase H) using mRNA fragments as templates, followed by second-strand cDNA synthesis using DNA polymerase I, RNAseH, buffer, and dNTPs. The synthesized double stranded cDNA fragments were then adapter-ligated for preparation of the paired-end library. Adaptor-ligate cDNA were used for PCR amplification. PCR products were purified (AMPure XP system) and library quality was assessed on an Agilent Bioanalyzer 4150 system. Finally, sequencing was performed with an Illumina Novaseq 6000 /MGISEQ-T7 instrument.

value: endometrium

value: endometriosis


title: ecopic endometrium, patient 11


title: ecopic endometrium, patient 9


title: WT Rep 2, Artemisinin treated


title: HCC- EVs treatment2 replicate2


title: HCC- EVs treatment1 replicate3

value: 1.2 mg/mL


title: HSC3 cells, suspended, 7th days, rep2


title: HCC- EVs treatment3 replicate3


title: ecopic endometrium, patient 7


title: CAL27 cells, adherent, at logarithmic period, rep2


title: HCC- EVs treatment3 replicate2


title: HCC+ EVs treatment3 replicate2


title: HCC+ EVs treatment3 replicate3


title: HCC- EVs treatment1 replicate2


title: HCC- EVs treatment1 replicate1


title: ecopic endometrium, patient 6


title: CAL27 cells, adherent, at logarithmic period, rep1


title: HCC+ EVs treatment2 replicate3


title: HCC+ EVs treatment2 replicate2


title: HCC- EVs treatment3 replicate1


title: HCC- EVs treatment2 replicate3


title: HCC- EVs treatment2 replicate1


title: ecopic endometrium, patient 8


title: eutopic endometrium, patient 6


title: HCC+ EVs treatment2 replicate1


title: HCC+ EVs treatment3 replicate1


title: Single B cell sequencing (scBCR-seq), LuS_RBD

city: Shanghai

first: Yuxuan

last: Zheng

address: 825 Zhangheng Rd.

institute: Fudan University

data_processing:
The raw single-cell BCR sequencing data were processed with subcommand vdj in 10× Genomics software CellRanger (version: 6.1.2), in which process the sequencing data were aligned into the mouse reference VDJ database (GRCm38).
Assembly: Mus musculus (GRCm38)
Supplementary files format and content: "filtered_contig.fasta" files include scBCR-seq filtered contigs, "filtered_contig_annotations.csv" files include annotated information of filtered contigs.

source_name: B cell

extract_protocol:
Single-cell suspensions were obtained by grinding the lymph nodes of immunized mice. The cells from each group of mice were pooled together. Antibodies used for staining were anti-mouse GL-7-FITC, CD138-PE, CD38-PE/Cy7, CD93-APC, B220-BV421 and IgD-BV510. All antibodies were used according to manufacturer's instructions. To stain the antigen-binding B cells, a mixture of SARS-CoV-2 RBD (Prototype), SARS-CoV-2 RBD (Beta), RaTG13 RBD, RshSTT182 RBD, LyRa11 RBD, RmYN02 RBD were used as baits by biotinylation via Biotin-Protein Ligase/BirA Enzyme (GeneCopoeia). BV711-Streptavidin was used to probe the biotinylated RBD. Antigen-specific BGC gated as GL-7+, B220high, CD38low, IgD-, CD93-, CD138- and RBD+ were sorted by BD FACS Aria II flow cytometer (BD Biosciences).
Antigen-specific B cells were sorted by flow cytometry and then subjected for high-throughput single-cell V(D)J sequencing with 10× Genomics platform. Brefly, after FACS sorting, cells were centrifuged, resuspended in 3% FBS (Sigma-Aldrich)/phosphate buffer solution (Thermo Fisher Scientific) and subjected to cell quality control using a cell counter. The cell viability of processed B cells was greater than 70%. After determining cell density, the single-cell library was constructed using a 10× Chromium Single Cell 5' Library and Gel Bead Kit following the manufacturer’s user guide. Cells were injected into three channels, aiming to achieve around 1,000-3,000 cells per channel. Gel beads-in-emulsion (GEMs) were formed in channels of a chip in the 10× Chromium instrument, and then collected in an Eppendorf plate for the GEM-reverse transcription (GEM-RT) reaction. After GEM clean up, GEM-RT products were subjected to two rounds of 9 and 15 PCR cycles using custom primers, followed by SPRI select (Beckman Coulter) bead clean up. Single-cell BCR V(D)J libraries were prepared following the manufacturer’s user guide, profiled using the Bioanalyzer High Sensitivity DNA kit (Agilent Technologies) and quantified with a Kapa Library Quantification Kit (Kapa Biosystems). Libraries were sequenced by paired-end sequencing (150-bp) on an Illumina NovaSeq (Illumina).

tag: vaccine

value: B cell


title: Serum, HC3-SYY, RNAseq

city: Ningbo

first: Yifang

last: Hu

address: fenghua road

institute: ningbo university

description: SYY

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.6.0)
The circRNA reads were aligned to reference genome using STAR(2.5.2b)detecting backesplicec junction reads with CIRCexplore2 (2.2.6)
Assembly: hg19
Supplementary files format and content: not provided; requested

source_name: serum

extract_protocol:
RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis
Total RNA of each sample was used to prepare the RNA sequencing library 1)RNA fragment；2)Random primed first strand cDNA synthesis；3)dUTP based second strand cDNA synthesis;4)Adaptor ligation and PCR amplification.

value: serum

tag: subject status

value: healthy control

value: hemocyte


title: Single B cell sequencing (scBCR-seq), LuS_mRBD_B


title: eutopic endometrium, patient 8


title: primary Leydig cells, dphp2

city: Nanjing

first: Yuhan

last: Ma

state: Jiangsu

address: Hankou Road 22

institute: Nanjing University

description: DPhP_2 FPKM

data_processing:
The raw data was filtered with SOAPnuke (v1.5.2) [1] by 1) Removing reads
containing adapters (adapter contamination); 2) Removing reads whose unknown base
('N' base) ratio is more than 10%; 3) Removing reads whose low-quality base ratio
(Base quality less than or equal to 15) is more than 50%, afterwards clean reads were
obtained and stored in FASTQ format.
Assembly: GRCm38.p6
Supplementary files format and content: xlsx. Files include FPKM values for each sample

source_name: testis

extract_protocol:
RNA was harvested using Trizol. 2 ug of total RNA was used for the construction of sequencing libraries.
A certain amount of RNA samples are denatured at suitable temperature to open their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads.The reaction system is configured. After reacting at the suitable temperature for a fixed period of time, RNAs are fragmented.Prepare the first-strand synthesis reaction system, and set up the reaction program, synthesize the first- strand cDNA, prepare the second-strand synthesis reaction system, and set up the reaction program to synthesize the second-strand cDNA.After the reaction system and program are configured and set up, double-stranded cDNA fragments are subjected to end-repair, and then a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments. The reaction system and program for adaptor ligation are subsequently configured and set up to ligate adaptors with the cDNAs.The PCR reaction system and program are configured and set up to amplify the product.

value: testis

value: primary Leydig cells

tag: genotype

value: WT

value: DPhP


title: primary Leydig cells, tphp1

description: TPhP_1 FPKM

value: TPhP


title: primary Leydig cells, dphp3

description: DPhP_3 FPKM


title: HCC+ EVs treatment1 replicate3


title: Serum, GDM3-WLL, RNAseq

description: WLL

value: gestational diabetes mellitus


title: Serum, GDM4-XHL, RNAseq

description: XHL


title: eutopic endometrium, patient 2


title: primary Leydig cells, dphp1

description: DPhP_1 FPKM


title: HCC+ EVs treatment1 replicate2


title: primary Leydig cells, ct3

description: Ct_3 FPKM

value: Control


title: HCC+ EVs treatment1 replicate1


title: eutopic endometrium, patient 1


title: eutopic endometrium, patient 5


title: primary Leydig cells, ct2

description: Ct_2 FPKM


title: primary Leydig cells, tphp3

description: TPhP_3 FPKM


title: Serum, HC4-WX, RNAseq

description: WX


title: ecopic endometrium, patient 1


title: Serum, HC2-LMF, RNAseq

description: LMF


title: primary Leydig cells, tphp2

description: TPhP_2 FPKM


title: eutopic endometrium, patient 4


title: control eutopic endometrium, patient 18

value: control


title: eutopic endometrium, patient 3


title: control eutopic endometrium, patient 16


title: o.EMVs derived from  passage 16 primary brain microvascular ECs

city: Zhanjiang

first: Huiting

last: Zhang

state: Guangdong

address: No. 57 People's Road South, Xiashan District

department: Neurological department

institute: The Affiliated Hospital of Guangdong Medical University

data_processing:
exceRpt was used to estimate the miRNA expression in miRBase
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: brain endothelial cells supernatant

extract_protocol:
RNA Isolation Total RNA from serum was isolated using miRNeasy Serum/Plasma Kit (QIAGEN) according to the protocol
Library preparation for small RNA Sequencing Small RNA library was prepared with approximately 100ng of total RNA using VAHTSTM Small RNA Library Prep Kit for Illumina® (Vazyme Biotech)

value: brain endothelial cells supernatant


title: Serum, GDM2-XPP, RNAseq

description: XPP


title: o.EMVs derived from  passage 15 primary brain microvascular ECs


title: Serum, GDM1-XBR, RNAseq

description: XBR


title: Spermine

first: Hongde

address: 150 Fucheng Road

institute: Hangzhou Institute of Medicine, Chinese Academy of Sciences

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg18 whole genome using bowtie v0.12.2.
Assembly: hg18
Supplementary files format and content: CSV file including FPKM values for each sample

source_name: Human macrophage

growth_protocol: Standard protocol

extract_protocol:
Total RNA from macrophages was isolated using TRIzol™ Plus RNA Purification Kit  and DNA was removed by treatment with TURBO DNA-free™ Kit.
RNA libraries for RNA-seq were prepared using Illumina Stranded mRNA Prep kit following manufacturer's protocols

treatment_protocol: 10 uM spermine for 48 hours

value: Human macrophage

value: Spermine


title: HaloTag-RPB1-70R 2/2

city: Coventry

first: Daniel

last: Hebenstreit

address: Gibbet Hill Rd

country: United Kingdom

institute: University of Warwick

description:
H70_kinetic_parameters_of_transcription.txt
H70.matrix.mtx.gz
H70.barcodes.tsv.gz
H70.features.tsv.gz

data_processing:
The Illumina base call files were demultiplexed with bcl2fastq Conversion Software (version 2.20)
The FASTQ files were randomly subsampled with seqtk to account for differences in sequencing depth. The fraction of reads subsampled for each sample was D25: 1.000000000, D52: 0.964703320, D70: 0.779511946, H25: 0.654947785, H52: 0.535025616, and H70: 0.543084659.
Assembly: Edited versions of the Genome Reference Consortium human build 38 (GRCh38) 2020 reference genome containing Dendra2 and HaloTag sequences as features
Supplementary files format and content: The kinetic_parameters_of_transcription.txt files list the mean expression (column Mean1), burst frequency (column K1), and squared coefficient of variation (column CV1) of each gene to 100 decimal places, estimated from fitting the negative-binomial model to the data from all cells that passed QC. Columns with the suffixes 0 and 2 list the 95% confidence intervals for the parameters.
Supplementary files format and content: The matrix.mtx.gz, barcodes.tsv.gz, and features.tsv.gz files are from the filtered_feature_bc_matrix directory generated by running the cellranger count pipeline on the subsampled FASTQ files.

source_name: Bone (osteosarcoma)

growth_protocol: Cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) at 37 °C and 5% CO2

extract_protocol:
Cells were harvested and washed according to the 10X Genomics sample preparation protocol (except 1X PBS with 0.5 % BSA was used instead of the suggested 1X PBS with 0.04 % BSA)
Droplet encapsulation and library preparation was performed by following the 10X Genomics Chromium Single cell 3' protocol using Chromium Next GEM Single Cell 3' GEM Library & Gel Bead Kit v3.1, Chromium Next GEM Chip G, and Dual Index Kit TT Set A. The cDNA amplification and sample index PCRs were performed with 12 and 11 cycles, respectively. The libraries were run with 1 % PhiX spike-in on a 150 cycle High v2.5 flow cell using the NextSeq 500 system (28 cycles for read 1, 10 cycles for index i7, 10 cycles for index i5, and 90 cycles for read 2)

treatment_protocol: Cells were incubated with α-amanitin (1 μg/ml) for six days before harvesting

value: Bone (osteosarcoma)

value: Epithelial cells

value: alpha-amanitin


title: HaloTag-RPB1-52R 2/2

description:
H52_kinetic_parameters_of_transcription.txt
H52.matrix.mtx.gz
H52.barcodes.tsv.gz
H52.features.tsv.gz


title: Control


title: primary Leydig cells, ct1

description: Ct_1 FPKM


title: HaloTag-RPB1-70R 1/2


title: Serum, HC1-GJ, RNAseq

description: GJ

value: serum


title: y.EMVs derived from  passage 2-3 primary brain microvascular ECs


title: HaloTag-RPB1-52R 1/2


title: HaloTag-RPB1-25R 1/2

description:
H25_kinetic_parameters_of_transcription.txt
H25.matrix.mtx.gz
H25.barcodes.tsv.gz
H25.features.tsv.gz


title: control eutopic endometrium, patient 13

value: endometrium


title: G26A-F3

status: Public on May 11 2024

city: London

first: Amanda

middle: Jean

last: Moehring

state: Ontario

address: 1151 Richmond Street, Western Science Centre 307

department: Biology

country: Canada

institute: Western University

description: Total RNA was extracted from 10 1-3 day-old virgin female flies

data_processing:
Sequence reads were obtained from Genewiz (South Plainfield, NJ)
Sequenced reads were trimmed for adaptor sequence and then mapped to Drosophila melanogaster reference genome (release r6.41_FB2021_04) using STAR v2.7.9a
Raw counts for each sample were obtained using featureCounts v2.0.0
Differentially expressed genes were determined using DESeq2 v1.42.0
Assembly: Drosophila melanogaster reference genome (release r6.41_FB2021_04)
Supplementary files format and content: RawCounts_AllSamples.csv: CSV file containing raw gene counts for every gene and every sample
Supplementary files format and content: NormalizedCounts_AllSamples.csv: CSV file containing normalized counts for all protein-coding genes for each sample

source_name: 10 whole flies

growth_protocol: Flies were separated by sex within 8 hours of eclosion to ensure virginity and aged 1-3 days before RNA extraction

extract_protocol:
RNA was extracted through TRIzol-chloroform method and DNA removed through dsDNAse treatment. Up to 20 micrograms of RNA was sent for sequencing.
Stranded Illumina TruSeq cDNA libraries with poly dT enrichment were prepared from high quality total RNA (RIN > 8)

treatment_protocol: 10 male OR female flies containing a wildtype serine tRNA OR a variant serine tRNA that misincorporates serine at proline codons

value: 10 whole flies

tag: Sex

value: female

value: w 1118; P{CaryP}attP40[v+=tRNA(Ser, UGG G26A)]/CyO, P{w+mC=2xTb1 -RFP}CyO; MKRS/TM6B, Tb1

value: Contains tRNA-Ser_UGG, G26A that misincorporates serine for proline


title: Dendra2-RPB1-52R 1/1

description:
D52_kinetic_parameters_of_transcription.txt
D52.matrix.mtx.gz
D52.barcodes.tsv.gz
D52.features.tsv.gz


title: G26A-M3

description: Total RNA was extracted from 10 1-3 day-old virgin male flies

value: male


title: Dendra2-RPB1-25R 1/1

description:
D25_kinetic_parameters_of_transcription.txt
D25.matrix.mtx.gz
D25.barcodes.tsv.gz
D25.features.tsv.gz


title: HaloTag-RPB1-25R 2/2


title: control eutopic endometrium, patient 17


title: control eutopic endometrium, patient 15


title: control eutopic endometrium, patient 14


title: y.EMVs derived from  passage 3-4 primary brain microvascular ECs


title: WT-F2

value: w 1118; P{CaryP}attP40[v+=tRNA(Ser, UGA)]/CyO, P{w+mC=2xTb1 -RFP}CyO; MKRS/TM6B, Tb1

value: Contains an extra copy of a wildtype tRNA-Ser_UGA_1-1


title: G26A-F2


title: G26A-F1


title: Dendra2-RPB1-70R 1/1

description:
D70_kinetic_parameters_of_transcription.txt
D70.matrix.mtx.gz
D70.barcodes.tsv.gz
D70.features.tsv.gz


title: WT-F3


title: WT-M3


title: WT-M2


title: WT-M1


title: G26A-M1


title: WT-F1


title: G26A-M2


title: M_control_151pk

type: protein

city: Rockville

first: Yu

last: Fan

state: MD

address: 9609 Medical Center Dr

institute: NCI/CBIIT

hyb_protocol: A SOMAmer-protein binding step is followed by a series of partitioning and wash steps to convert relative epitope concentrations into measurable nucleic acid signals that are quantified using DNA-hybridization microarrays

scan_protocol: The cyanine-3 signal from the SOMAmer reagent is detected on microarrays

data_processing: Intraplate and interplate variations were adjusted by SOMAscan® v4 Data Standardization pipeline. Log2(data +1) transformation was performed before all downstream analysis.

label: biotin

molecule: protein

source_name: plasma collected after irradiation

label_protocol: SOMAmer® (Slow Off-rate Modified Aptamer) reagents which consist of short single-stranded DNA sequences that incorporate hydrophobic modifications

growth_protocol: nine to eleven week old female or male C57BL6 mice received a single total body irradiation (TBI) dose of 2, 4, or 8 Gy or sham radiation.  All mice receiving TBI were confined unanesthetized in plexiglass containers.  All animal studies were conducted in accordance with the principles and procedures outlined in the NIH Guide for the Care and Use of Animals and procedures were approved by the NIH Lab Animal Safety Program under an approved protocol #ROB170.

extract_protocol: Approximately 140ul of plasma per sample was used for the Somalogic SomaScan Assay

treatment_protocol: Murine in vivo models utilized a Precision X-ray source at a dose rate of 407 cGy/min. Dose rate was calibrated based upon the procedures described in American Association of Physicist in Medicine (AAPM) Task Group Report 61 (TG-61) with regard to the following conditions:  X-ray tube potential was 320 kV, half value layer (HVL) is 0.8 mm Copper (Cu), source to surface distance (SSD) was 50 cm.  Dose rate was measured at 2 cm depth in solid water phantom using a PTW model: N23342 ion chamber and Inovision, model 35040 electrometer.

tag: strain

value: plasma

tag: gender

value: M

tag: dose

tag: timepoint


title: M_control_146pk

value: control


title: M_control_145pk


title: M_control_159pk


title: M_control_153pk


title: M_control_154pk


title: M_control_150pk


title: M_control_152pk


title: M_control_155pk


title: M_control_144pk


title: M_control_143pk


title: M_control_147pk


title: M_control_160pk


title: M_control_149pk


title: M_control_156pk


title: M_control_157pk


title: M_control_158pk


title: M_control_141pk


title: M_control_148pk


title: M_8Gy_Day7_140pk


title: M_8Gy_Day7_135pk


title: M_8Gy_Day7_138pk


title: M_8Gy_Day3_120pk


title: 24hr MVA infected RNA-seq Bio rep 2

city: Los Alamos

first: Christina

middle: Rene

last: Steadman

state: New Mexico

address: Bikini Atoll Rd

department: Earth & Environmental Sciences Division

institute: Los Alamos National Laboratory

description: 2501_139-UDP0082-_ACCGTTACAA-CTCATAGCGA__S12_R1_PAIREDAligned.out.sam.counts

data_processing:
The Chlorocebus sabaeus reference genome was retrieved from NCBI (GCF_000409795.2) andappended with the vaccinia virus (VACV) genome, retrieved from GenBank (U94848.1).Genome annotations for C. sabaeus were downloaded from NCBI and the GenBank flat fileannotations for VACV were retrieved using the bio package command (bio fetch U94848.1 --format gff) and converted to gtf format using the AGAT package function(agat_convert_sp_gff2gtf.pl). The C. sabaeus annotation was appended with the VACVannotation for subsequent analysis. Raw read quality control was performed using FastQC andSeqMonk to verify library quality and degree of PCR duplication. All metrics were normal. Asplice junction aware reference index was generated for the combined genome and annotationfiles using STAR with the arguments (--runMode genomeGenerate --sjdbOverhang 149). Prealignmentread trimming was not performed in favor of soft-clipping/quality filtering by theSTAR aligner. Reads were aligned to the combined genome using STAR. Duplicate reads weremarked but retained in downstream analysis per DESeq2 usage guidelines. Sense strand readsaligning to gene features were counted using htseq-count with the arguments (--stranded=reverse). Antisense strand reads aligning to gene features were counted using htseqcountwith the arguments (--stranded=yes). Differential expression analysis was performed usingthe DESeq2 matrix design (~time + treatment). For visualization, replicate alignment files weremerged using samtools. bigWigs were then generated using the bamCoverage function from thedeepTools package with the arguments (--effectiveGenomeSize 2836634000 --normalizeUsingBPM –filterRNAstrand {forward/reverse/NULL} --binSize 1).
Assembly: The Chlorocebus sabaeus reference genome (GCF_000409795.2) appended with the vaccinia virus (VACV) genome, retrieved from GenBank (U94848.1)
Supplementary files format and content: Strand specific read pileup in bigwig format. Including vaccinia virus genome.
Supplementary files format and content: Processed data given as supplementary files include DESEQ2 result files for various comparions. In file named UTR indicates Mock infected control and V indicates MVA infected sample. Futher, time point is mentioned in the file name to indicate the timepoints compared in each file. Comparison is made by considering control as the denominator or ealier timepoint as the denominator.

organism: Chlorocebus sabaeus

source_name: Kidney derived cell line

growth_protocol: Cryopreserved Vero cells, derived from the kidney tissue of a normal adult African greenmonkey, were sourced from the ATCC (Cat # CCL-81). Cells were thawed, passaged, expanded,and seeded for viral infection in complete medium consisting of Dulbecco’s Modified Eagle’sMedium (DMEM) containing 4 mM L-Glutamine (ATCC, Cat # 30-2002), supplemented with10% (v/v) Fetal Bovine Serum (FBS, ATCC, Cat # 30-2020) and filter-sterilized beforeuse. Vero cells were maintained at 37°C with 5% CO2 and 95% relative humidity. Vero cellswere cryopreserved at passage #7 from the original source vial using freeze medium consistingof DMEM supplemented with 10% (v/v) FBS and 5% (v/v) dimethylsulfoxide (DMSO, ATCC,Cat # 4-X).

extract_protocol:
Cells were harvested in two biological replicates (A and B) per condition (mock-infected andMVA-infected) at each timepoint (12 hrs, 18 hrs, and 24 hrs post-infection). At each timepoint,cells were washed using 1X phosphate-buffered saline (PBS, Gibco, Cat # 10010049), detachedfor 15 min at 37°C using 1X TrypLE Express Enzyme (Gibco, Cat # 12604021), andresuspended in pre-warmed complete medium before cell counting with the Scepter 3.0Handheld Cell Counter and 60 μm Counter Sensors. At each timepoint, mock-infected andMVA-infected cell suspensions were divided and processed for Hi-C, ATAC-seq and RNA-seqtechniques
For RNA-seq, 2x10^5 cells were cryopreserved in duplicate 1 mL aliquots using freeze mediumon the day of cell harvest. Aliquots were subsequently thawed in a 37°C water-bath into ice-coldcomplete medium, then pelleted by centrifugation, washed in ice-cold HBSS, and resuspended in350 μL ice-cold RULT Buffer (Qiagen, Cat # 73934) containing 1% beta-mercaptoethanol(Sigma, Cat #63689). RNA was extracted from these cell lysates using the RNeasy UCP MicroKit protocol and reagents (Qiagen, Cat #73934). DNA was digested via on-column DNase Itreatment for 15 min at room temperature. RNA extracts were eluted in 20 μL RNase-free water.The concentration of total RNA was determined using the Qubit RNA HS Assay Kit(ThermoFisher Scientific, Cat # Q32855) and quality was measured using the Bioanalyzer RNA6000 Assay (Agilent, Cat. # 5067-1511). Ribosomal RNA was depleted from 500 ng total RNAusing the Illumina Ribo-Zero Plus rRNA Depletion Kit (Illumina, Cat. # 20037135). RNA wasconverted to cDNA, and adapters and indexes were added onto the ends of the fragments togenerate strand specific Illumina libraries. Libraries were eluted in DNA Elution Buffer (ZymoResearch, Cat #D3004-4-10). The concentration and average size of the libraries was verifiedusing the TapeStation DNA 5000 Assay Reagents and Screen Tapes (Agilent, Cat. # 5067-5589and 5067-5588). Libraries were normalized and pooled based on the TapeStation concentrations.An accurate library quantification of the pool was determined using the Illumina/Universal Kit(KAPA Biosystems, KK4824). The pool was sequenced on an entire lane of a NextSeq 500 HOflow cell to generate paired-end 151 bp reads using the NextSeq 500 High Output Kit v2.5 (300cycles) (Illumina, Cat # 20024908).

treatment_protocol: Cryopreserved Vero cells were thawed at passage #8 and propagated for 2 passages prior toseeding for viral infection. At the time of seeding, a cell suspension was made in pre-warmedcomplete medium and digitally counted using the Scepter 3.0 Handheld Cell Counter and 60 μmCounter Sensors (Millipore, Cat # PHCC360KIT). Cells were seeded for viral infection atpassage #11 into replicate tissue culture flasks and multi-well plates using 5x10^6 cells per T175flask or 5x10^5 cells per well in 12-well plates. Seeded flasks and plates were incubated for 24 hrsat 37°C, yielding ~1x10^7 cells per flask and ~1x10^6 cells per well at the time of infection. Modified Vaccinia Ankara virus, strain VACV-MVA, was obtained from the ATCC (Cat # VR-1508). VACV-MVA viral stock was diluted in infection medium consisting of DMEM31supplemented with 2% (v/v) FBS. Vero cells were infected at 0 hrs using 0.4 MOI in a minimalvolume of inoculum (3 mL per flask) for 1 hr at 37°C; 17 mL infection medium was added priorto incubation for 12-24 hrs at 37°C. In parallel to the flasks, 12-well plates for ICC staining andcell imaging were also infected in parallel to the flasks at 0 hr using 0.4 MOI in 300 μL per well;then 700 μL infection medium was added prior to incubation for 12-24 hrs at 37°C.

value: Kidney derived cell line

value: Vero CCL-81

value: 24hr MVA infected


title: M_8Gy_Day7_139pk


title: M_8Gy_Day3_118pk


title: M_8Gy_Day3_122pk


title: 18hr MVA infected RNA-seq Bio rep 1

description: 2501_134-UDP0077-_TCTGGTATCC-CGTTGCTTAC__S23_R1_PAIREDAligned.out.sam.counts

value: 18hr MVA infected


title: 24hr MVA infected RNA-seq Bio rep 1

description: 2501_138-UDP0081-_TGTCGCTGGT-TCGTCTGACT__S9_R1_PAIREDAligned.out.sam.counts


title: 24hr Mock infected RNA-seq Bio rep 2

description: 2501_137-UDP0080-_GGCAAGCCAG-CAAGCATCCG__S6_R1_PAIREDAligned.out.sam.counts

value: 24hr Mock infected


title: M_8Gy_Day3_121pk


title: M_8Gy_Day7_136pk


title: M_8Gy_Day7_137pk


title: M_8Gy_Day3_119pk


title: M_control_142pk


title: M_8Gy_Day1_104pk


title: M_8Gy_Day3_117pk


title: 24hr Mock infected RNA-seq Bio rep 1

description: 2501_136-UDP0079-_ACGGTCAGGA-CGGCCTCGTT__S3_R1_PAIREDAligned.out.sam.counts


title: 18hr Mock infected RNA-seq Bio rep 2

description: 2501_133-UDP0076-_CTGACTCTAC-ACGGCCGTCA__S19_R1_PAIREDAligned.out.sam.counts

value: 18hr Mock infected


title: 18hr MVA infected RNA-seq Bio rep 2

description: 2501_135-UDP0078-_CATTAGTGCG-TGACTACATA__S26_R1_PAIREDAligned.out.sam.counts


title: 18hr Mock infected RNA-seq Bio rep 1

description: 2501_132-UDP0075-_CTCTGCAGCG-GATGGATGTA__S15_R1_PAIREDAligned.out.sam.counts


title: M_8Gy_Day1_101pk


title: M_8Gy_Day1_103pk


title: M_8Gy_Day1_100pk


title: M_4Gy_Day7_131pk


title: M_4Gy_Day7_134pk


title: M_8Gy_Day1_99pk


title: M_4Gy_Day7_132pk


title: gastrocnemius_mdx_CHP_rep4

city: Lausanne

first: Keno

last: Strotjohann

address: Route Cantonale

department: School of Life Sciences, Institute of Bioengineering

country: Switzerland

institute: École Polytechnique Fédérale de Lausanne (EPFL)

description:
83
raw_counts_gastrocnemius_dmd.csv

data_processing:
After sequencing, the raw reads were filtered by removing adaptor sequences, contamination and low-quality (RIN <8) reads from the raw reads.
All samples passed quality check by FastQC.
Sequenced reads were mapped to the GRCm38 mm10 primary assembly of the mouse genome using ensembl release 95 gene annotation with STAR aligner version 2.6.0a.
Reads were counted using STAR aligner.
Assembly: mm10
Supplementary files format and content: csv file with raw counts for each gene and sample

source_name: Gastrocnemius

extract_protocol:
For the DMD study, RNA was extracted in Trizol (TriPure, Roche) from frozen ventricles or GM tissue, using the NucleoSpin RNA extraction kit (Macherey-Nagel). From age mice, total RNA was extracted from GM using NucleoZOL reagent (740404.200, Macherey-Nagel).
RNA libraries were prepared for sequencing using standard protocols with polyA enrichment.
Paired-end RNA sequencing was performed using BGISEQ-500 for the DMD study and Illumina NovaSeq for the aging study.

treatment_protocol: Mdx mice were treated from week 7 to week 22 of age with CHP at a dose of 35 mg/kg or water as control,  BL10 mice received water (control), three times per week by oral gavage. 18-month-old male C57BL6/J mice received DW or CHP (35mg/kg/day) orally for 6 months.

value: Gastrocnemius

value: CHP


title: gastrocnemius_mdx_CHP_rep5

description:
84
raw_counts_gastrocnemius_dmd.csv


title: gastrocnemius_mdx_CHP_rep3

description:
82
raw_counts_gastrocnemius_dmd.csv


title: M_8Gy_Day1_102pk


title: 12hr MVA infected RNA-seq Bio rep 1

description: 2501_130-UDP0073-_CCTGCGGAAC-ATCATAGGCT__S8_R1_PAIREDAligned.out.sam.counts

value: 12hr MVA infected


title: gastrocnemius_mdx_CHP_rep2

description:
80
raw_counts_gastrocnemius_dmd.csv


title: M_4Gy_Day7_133pk


title: gastrocnemius_mdx_ctrl_rep4

description:
75
raw_counts_gastrocnemius_dmd.csv

value: water


title: 12hr Mock infected RNA-seq Bio rep 1

description: 2501_128-UDP0071-_CTTGTACACC-AAGCGCGCTT__S2_R1_PAIREDAligned.out.sam.counts

value: 12hr Mock infected


title: gastrocnemius_mdx_CHP_rep1

description:
78
raw_counts_gastrocnemius_dmd.csv


title: gastrocnemius_mdx_ctrl_rep5

description:
76
raw_counts_gastrocnemius_dmd.csv


title: 12hr Mock infected RNA-seq Bio rep 2

description: 2501_129-UDP0072-_ACACAGGTGG-TGAGCGTTGT__S5_R1_PAIREDAligned.out.sam.counts


title: M_4Gy_Day7_130pk


title: gastrocnemius_mdx_ctrl_rep3

description:
74
raw_counts_gastrocnemius_dmd.csv


title: M_4Gy_Day7_129pk


title: Day_12_FSHD2_4_R2 [methylation]

city: Irvine

first: Ali

last: Mortazavi

address: 2300E Biological Sciences 3

institute: UC Irvine

description: PerMeth.AllRegions.csv

data_processing:
Raw data converted to fastq using bcl2fastq v2.18.0.12 from Illumina.
Raw reads from TruSeq Methyl Capture EPIC libraries were mapped to canonical chromosomes from hg38 and the patch region of D4Z4 (chr4_KQ983257v1_fix) using bismark (version 0.19.0).
Sites were extracted from the bam file using bismark_methylation_extractor with paired end and no overlap specified. To remove bias from the ends of reads, 2 bp from the 5’ end of read 2 and 1 bp from the 3’ end of read 1 were ignored when extracting sites.
All CpG sites were read into methylKit (version 1.16.0). Sites within 200 bp were merged into one region using bumphunter (version 1.32.0). Methylation over those regions was summarized using regionCounts and filtered for at least three CpG sites.
Regions were then filtered for a coverage of at least 5. Regions were normalized using normalizeCoverage, and only regions with coverage in all samples were kept.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: *.bismark.cov: Coverage files are output from bismark and contain the 0-indexed site, percent methylation, number of methylated sites and number of unmethylated sites in that order.
Supplementary_files_format_and_content: PerMeth.AllRegions.csv: Percent methylation file contains the percent methylation for regions per sample normalized as described above.

source_name: Primary myoblasts from quadricep biopsy

extract_protocol:
Genomic DNA was collected from a single 6 cm dish using the DNeasy Blood & Tissue kit (69504, Qiagen).
All DNA methylation data was generated using the TruSeq Methyl Capture EPIC kit (FC-151-1003, Illumina) according to manufacturer’s protocol.
Libraries were sequenced on the Illumina NextSeq500 with paired-end 75 bp reads to a depth of 20 to 82 million reads.

value: Myoblasts

tag: muscle group

value: quadricep

tag: fshd status

tag: day of differentiation

value: Day 12


title: 12hr MVA infected RNA-seq Bio rep 2

description: 2501_131-UDP0074-_TTCATAAGGT-TGTTAGAAGG__S11_R1_PAIREDAligned.out.sam.counts


title: gastrocnemius_mdx_ctrl_rep1

description:
71
raw_counts_gastrocnemius_dmd.csv


title: gastrocnemius_mdx_ctrl_rep2

description:
73
raw_counts_gastrocnemius_dmd.csv


title: Day_12_FSHD2_4_R1 [methylation]

description: PerMeth.AllRegions.csv


title: Day_3_FSHD2_4_R2 [methylation]

description: PerMeth.AllRegions.csv

value: Day 3


title: gastrocnemius_BL10_ctrl_rep5

description:
69
raw_counts_gastrocnemius_dmd.csv


title: M_4Gy_Day3_114pk

value: plasma

value: M


title: gastrocnemius_BL10_ctrl_rep4

description:
67
raw_counts_gastrocnemius_dmd.csv


title: gastrocnemius_BL10_ctrl_rep3

description:
66
raw_counts_gastrocnemius_dmd.csv


title: gastrocnemius_BL10_ctrl_rep2

description:
65
raw_counts_gastrocnemius_dmd.csv


title: heart_mdx_CHP_rep5

description:
63
raw_counts_heart_dmd.csv

source_name: Ventricle

value: Ventricle


title: Day_3_FSHD2_4_R1 [methylation]

description: PerMeth.AllRegions.csv


title: Day_0_FSHD2_4_R2 [methylation]

description: PerMeth.AllRegions.csv

value: Day 0


title: heart_mdx_CHP_rep4

description:
62
raw_counts_heart_dmd.csv


title: M_4Gy_Day3_115pk


title: heart_mdx_CHP_rep3

description:
59
raw_counts_heart_dmd.csv


title: heart_mdx_CHP_rep2

description:
58
raw_counts_heart_dmd.csv


title: M_4Gy_Day3_116pk


title: Day_0_FSHD2_4_R1 [methylation]

description: PerMeth.AllRegions.csv


title: Day_12_FSHD2_3_R2 [methylation]

description: PerMeth.AllRegions.csv


title: gastrocnemius_BL10_ctrl_rep1

description:
64
raw_counts_gastrocnemius_dmd.csv


title: M_4Gy_Day3_113pk


title: heart_mdx_ctrl_rep5

description:
55
raw_counts_heart_dmd.csv


title: heart_mdx_ctrl_rep4

description:
54
raw_counts_heart_dmd.csv


title: M_4Gy_Day1_98pk


title: Day_12_FSHD2_3_R1 [methylation]

description: PerMeth.AllRegions.csv


title: heart_mdx_ctrl_rep3

description:
53
raw_counts_heart_dmd.csv


title: M_4Gy_Day3_111pk


title: heart_mdx_ctrl_rep2

description:
52
raw_counts_heart_dmd.csv


title: heart_mdx_CHP_rep1

description:
57
raw_counts_heart_dmd.csv


title: M_4Gy_Day1_97pk


title: heart_mdx_ctrl_rep1

description:
50
raw_counts_heart_dmd.csv


title: heart_BL10_ctrl_rep5

description:
48
raw_counts_heart_dmd.csv


title: Day_3_FSHD2_3_R2 [methylation]

description: PerMeth.AllRegions.csv


title: heart_BL10_ctrl_rep4

description:
46
raw_counts_heart_dmd.csv


title: Day_3_FSHD2_3_R1 [methylation]

description: PerMeth.AllRegions.csv


title: M_4Gy_Day1_94pk


title: heart_BL10_ctrl_rep2

description:
44
raw_counts_heart_dmd.csv


title: M_4Gy_Day3_112pk


title: Day_0_FSHD2_3_R2 [methylation]

description: PerMeth.AllRegions.csv


title: heart_BL10_ctrl_rep1

description:
43
raw_counts_heart_dmd.csv


title: M_4Gy_Day1_93pk


title: Day_0_FSHD2_3_R1 [methylation]

description: PerMeth.AllRegions.csv


title: Tbx1-/- rep 4

city: Naples

first: Antonio

last: Baldini

state: Naples

address: Via Sergio Pansini 5

department: Department of Molecular Medicine and Medical Biotechnology

country: Italy

institute: University of Naples Federico II

data_processing:
Sequence reads were trimmed using bbduk softwareto remove adapter sequences, poly-A tails and low-quality end bases (regions with average quality below 6)
Alignment was performed with STAR on the reference genome mm10 provided by UCSC Genome Browser
The expression levels of genes were determined with featureCounts from Rsubread counting the reads that align to the forward strand
To account for biological variability, we used the noiseqbio function, setting the cutoff for the posterior probability to 0.95, to identify the differentially expressed genes. Gene ontology of the differentially expressed genes was performed with the gprofiler online tool (https://biit.cs.ut.ee/gprofiler/gost) using the entire set of expressed genes as the background.
Assembly: mm10
Supplementary files format and content: tab delimited text file includes raw count for each sample

source_name: E14-Tg2a 4D

growth_protocol: The culture medium consisted of GMEM (Sigma Cat# G5154) supplemented with 10^3 U/ml ESGRO LIF (Millipore, Cat# ESG1107), 15% fetal bovine serum (ES Screened Fetal Bovine Serum, US Euroclone Cat# CHA30070L), 0.1 mM non-essential amino acids (Gibco, Cat# 11140-035), 0.1 mM 2-mercaptoethanol (Gibco, Cat# 31350-010), 0.1 mM L-glutamine (Gibco, Cat# 25030081), 0.1 mM Penicillin/Streptomycin (Gibco, Cat# 10378016), and 0.1 mM sodium pyruvate (Gibco, Cat# 11360-070).

extract_protocol:
Qiagen RNeasy micro/mini plus Kit for RNA isolation and provide 10 μl of RNA at the exact concentration of 50 ng/μL
Quantseq 3′-biased protocol

treatment_protocol: Cell Differentiation in precardiac mesoderm according to the paper by Andersen et al Nat Commun 9, 3140 (2018)

value: E14-Tg2a 4D

value: in vitro differentiation


title: M_4Gy_Day1_95pk


title: Tbx1-/- rep 3


title: M_2Gy_Day7_128pk


title: Day_12_Control_4_R2 [methylation]

description: PerMeth.AllRegions.csv

value: Control


title: Tbx1-/- rep 2


title: Tbx1-/- rep 1


title: Day_12_Control_4_R1 [methylation]

description: PerMeth.AllRegions.csv


title: WT rep 3

value: WT


title: WT rep 4


title: WT rep 2


title: Day_3_Control_4_R2 [methylation]

description: PerMeth.AllRegions.csv


title: M_4Gy_Day1_96pk


title: Day_3_Control_4_R1 [methylation]

description: PerMeth.AllRegions.csv


title: M_2Gy_Day7_127pk


title: WT rep 1


title: heart_BL10_ctrl_rep3

description:
45
raw_counts_heart_dmd.csv


title: M_2Gy_Day7_126pk


title: M_2Gy_Day7_125pk


title: CKO_HFD_8

first: Jiani

last: Lu

address: No.85 Wujin Rd.

institute: Shanghai General Hospital

data_processing:
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. Clean reads were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data.  All the downstream analyses were based on the clean data with high quality.
Paired-end clean reads were aligned to mm10 using Hisat2 (v2.0.5). FeatureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes read counts for each sample

source_name: skeletal muscle

extract_protocol:
The RNA was isolated using Trizol method.
Libraries were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols

value: skeletal muscle

value: CSE KO

value: HFD diet


title: CKO_HFD_6


title: M_2Gy_Day7_124pk


title: Day_0_Control_4_R2 [methylation]

description: PerMeth.AllRegions.csv


title: CKO_HFD_5


title: Day_0_Control_4_R1 [methylation]

description: PerMeth.AllRegions.csv


title: CKO_HFD_4


title: Day_12_Control_3_R2 [methylation]

description: PerMeth.AllRegions.csv


title: CKO_HFD_2


title: CKO_HFD_3


title: M_2Gy_Day7_123pk


title: Day_12_Control_3_R1 [methylation]

description: PerMeth.AllRegions.csv


title: WT_HFD_8


title: M_2Gy_Day3_109pk


title: CKO_HFD_1


title: M_2Gy_Day3_110pk


title: WT_HFD_6


title: Day_3_Control_3_R2 [methylation]

description: PerMeth.AllRegions.csv


title: WT_HFD_5


title: CKO_HFD_7


title: Day_3_Control_3_R1 [methylation]

description: PerMeth.AllRegions.csv


title: M_2Gy_Day3_108pk


title: WT_HFD_3


title: WT_HFD_4


title: Day_0_Control_3_R2 [methylation]

description: PerMeth.AllRegions.csv


title: WT_HFD_2


title: M_2Gy_Day3_107pk


title: WT_HFD_1


title: Day_0_Control_3_R1 [methylation]

description: PerMeth.AllRegions.csv


title: CKO_chow_8

value: Chow diet


title: M_2Gy_Day3_106pk


title: Day_12_FSHD2_1_R2 [methylation]

description: PerMeth.AllRegions.csv

source_name: Primary myoblasts from tibialis anterior biopsy

value: tibialis anterior


title: CKO_chow_7


title: CKO_chow_5


title: WT_HFD_7


title: M_2Gy_Day1_92pk


title: M_2Gy_Day1_91pk


title: CKO_chow_3


title: M_2Gy_Day1_90pk


title: Day_3_FSHD2_1_R2 [methylation]

description: PerMeth.AllRegions.csv

value: Myoblasts


title: CKO_chow_1


title: CKO_chow_2


title: Day_3_FSHD2_1_R1 [methylation]

description: PerMeth.AllRegions.csv


title: WT_chow_8


title: M_2Gy_Day1_89pk


title: WT_chow_7


title: WT_chow_5


title: Day_0_FSHD2_1_R2 [methylation]

description: PerMeth.AllRegions.csv


title: WT_chow_6


title: M_2Gy_Day3_105pk


title: Day_0_FSHD2_1_R1 [methylation]

description: PerMeth.AllRegions.csv


title: WT_chow_4


title: WT_chow_3


title: CKO_chow_6


title: Day_12_FSHD2_1_R1 [methylation]

description: PerMeth.AllRegions.csv


title: M_2Gy_Day1_88pk


title: F_control_86pk

value: F

value: control


title: M_2Gy_Day1_87pk


title: WT_chow_2


title: Day_12_FSHD2_2_R2 [methylation]

description: PerMeth.AllRegions.csv

value: Day 12


title: CKO_chow_4


title: Day_12_FSHD2_2_R1 [methylation]

description: PerMeth.AllRegions.csv


title: tibialis_aged_CHP_rep4

description:
TA12
raw_counts_tibialis_aged.csv

source_name: Tibilalis anterior

value: Tibilalis anterior

value: CHP


title: tibialis_aged_CHP_rep3

description:
TA8
raw_counts_tibialis_aged.csv


title: F_control_84pk

value: plasma


title: WT_chow_1


title: tibialis_aged_CHP_rep1

description:
TA6
raw_counts_tibialis_aged.csv


title: Day_3_FSHD2_2_R2 [methylation]

description: PerMeth.AllRegions.csv

value: Day 3


title: Day_3_FSHD2_2_R1 [methylation]

description: PerMeth.AllRegions.csv


title: tibialis_aged_CHP_rep2

description:
TA7
raw_counts_tibialis_aged.csv


title: tibialis_aged_ctrl_rep4

description:
TA5
raw_counts_tibialis_aged.csv

value: water


title: Day_0_FSHD2_2_R2 [methylation]

description: PerMeth.AllRegions.csv

value: Day 0


title: tibialis_aged_ctrl_rep3

description:
TA4
raw_counts_tibialis_aged.csv


title: F_control_82pk


title: F_control_85pk


title: F_control_83pk


title: tibialis_aged_ctrl_rep2

description:
TA3
raw_counts_tibialis_aged.csv


title: tibialis_aged_ctrl_rep1

description:
TA1
raw_counts_tibialis_aged.csv


title: Day_0_FSHD2_2_R1 [methylation]

description: PerMeth.AllRegions.csv


title: Day_12_Control_2_R2 [methylation]

description: PerMeth.AllRegions.csv

value: Control


title: Day_12_Control_2_R1 [methylation]

description: PerMeth.AllRegions.csv


title: Day_3_Control_2_R2 [methylation]

description: PerMeth.AllRegions.csv


title: Day_3_Control_2_R1 [methylation]

description: PerMeth.AllRegions.csv


title: Day_0_Control_2_R2 [methylation]

description: PerMeth.AllRegions.csv


title: F_control_80pk


title: F_control_78pk


title: F_control_77pk


title: F_control_79pk


title: F_control_81pk


title: F_control_76pk


title: Day_12_Control_1_R2 [methylation]

description: PerMeth.AllRegions.csv


title: F_control_75pk


title: Day_0_Control_2_R1 [methylation]

description: PerMeth.AllRegions.csv


title: F_control_60y


title: F_control_73pk


title: F_control_74pk


title: Day_3_Control_1_R2 [methylation]

description: PerMeth.AllRegions.csv


title: Day_3_Control_1_R1 [methylation]

description: PerMeth.AllRegions.csv


title: F_control_59y


title: Day_12_Control_1_R1 [methylation]

description: PerMeth.AllRegions.csv


title: F_control_58y


title: F_control_57y


title: Day_0_Control_1_R2 [methylation]

description: PerMeth.AllRegions.csv


title: 207760740001_R10C03

type: genomic

city: Philadelphia

first: Wanding

last: Zhou

state: PA

address: 3501 Civic Center Blvd

department: Pathology and Lab Medicine

institute: Children's Hospital of Philadelphia

description: motor cortex

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing: SeSAMe software v1.22, openSesame and IDATs are de-identified to mask SNP probe readings

label: Cy5 and Cy3

source_name: Human primary cell DNA

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from 30-70 mg of tissue or 5.0 x 10^6 cells for cell lines using commercially available QIAGEN QIAamp Mini Kit (QIAGEN, 51304), following the manufacturer’s protocol. DNA was quantified using a Qubit 4 Fluorometer (Invitrogen).


title: F_control_56y


title: 207760740001_R14C03

description: cerebellum


title: Day_0_FSHD1_2_R2

data_processing:
Raw data converted to fastq using bcl2fastq v2.18.0.12 from Illumina.
Reads were mapped to hg38 by STAR (version 2.5.1b) using defaults except with a maximum of 10 mismatches per pair, a ratio of mismatches to read length of 0.07, and a maximum of 10 multiple alignments.
Quantitation was performed using RSEM (version 1.2.31) with defaults with gene annotations for protein coding genes and lncRNAs from GENCODE v28. Results were output as counts, and effective gene length was used after normalization to compute transcripts per million (TPM).
Counts were batch corrected for the two different library prep methods using ComBat-seq from sva (version 3.36.0).
Genes were filtered for 10 counts in all samples of at least one condition (same FSHD status, muscle group and differentiation day) using filterByExpr from edgeR (version 3.30.3).
Genome_build: hg38
Supplementary_files_format_and_content: RSEM output tab-delimited text files with abundance measures in counts and TPM.

extract_protocol:
Cells were lifted using trypsin. Total RNA was extracted by using the RNeasy kit (QIAGEN).
RNA was converted to cDNA using the Smart-Seq 2 protocol (Picelli, et al., Nat. Protoc., 2014). Libraries were constructed with the Nextera DNA Library Prep Kit (Illumina) for days 0 to 5 for FSHD2-3. The Nextera DNA Flex Library Prep Kit (Illumina) was used for all other RNA-seq samples. Libraries were sequenced on the Illumina NextSeq500 with paired-end 43 bp reads to a depth of 5 to 40 million reads.

tag: muscle source

tag: library prep kit

value: Nextera DNA Flex Library Prep Kit (20018704, Illumina)


title: Day_0_Control_1_R1 [methylation]

description: PerMeth.AllRegions.csv

tag: cell line


title: 207760740001_R12C03

description: motor cortex


title: 207760740001_R04C03

description: NK cells


title: 207760740001_R02C03

description: Monocytes


title: 207760740001_R03C03

description: CD4+ T cells


title: F_8Gy_Day7_36y

tag: tissue


title: 207760740001_R16C03

description: cerebellum


title: 207760740001_R01C03

description: Total T cells


title: 207760740001_R08C03

description: motor cortex


title: 207760740001_R13C03

description: CD4+ T cells


title: 207760740001_R14C02

description: NK cells


title: 207760740001_R06C03

description: PBMC


title: 207760740001_R09C03

description: PBMC


title: 207760740001_R07C03

description: Monocytes


title: 207760740001_R05C03

description: CD8+ T cells


title: 207760740001_R16C02

description: PBMC


title: 207760740001_R11C03

description: Total T cells


title: 207760740001_R15C03

description: CD8+ T cells


title: 207760740001_R04C02

description: colon


title: Day_0_FSHD1_1_R2


title: Day_0_FSHD1_2_R1


title: 207760740001_R12C02

description: Monocytes


title: 207760740001_R10C02

description: Total T cells


title: F_8Gy_Day7_34y


title: 207760740001_R08C02

description: heart


title: F_control_55y


title: 207760740001_R15C02

description: colon


title: F_8Gy_Day7_35y


title: 207760740001_R02C02

description: colon


title: F_8Gy_Day7_33y


title: Day_0_FSHD1_1_R1


title: Day_5_FSHD2_3_R1

value: Day 5

value: quadricep

value: Nextera DNA Library Prep Kit (FC-121-1030, Illumina)


title: Day_4_FSHD2_3_R2

value: Day 4


title: F_8Gy_Day7_32y


title: 207760740001_R11C02

description: colon


title: Day_4_FSHD2_3_R1


title: F_8Gy_Day7_31y


title: 207760740001_R07C02

description: CD4+ T cells


title: Day_5_FSHD2_3_R2


title: F_8Gy_Day3_29y


title: F_8Gy_Day3_30y


title: Day_3_FSHD2_3_R1


title: F_8Gy_Day3_28y


title: Day_2_FSHD2_3_R2

value: Day 2


title: 207760740001_R16C01

description: pancreas


title: Day_3_FSHD2_3_R2


title: F_8Gy_Day3_27y


title: F_8Gy_Day3_26y


title: Day_2_FSHD2_3_R1


title: 207760740001_R09C02

description: colon


title: 207760740001_R03C02

description: colon


title: Day_1_FSHD2_3_R2

value: Day 1


title: 207760740001_R01C02

description: colon